Next Article in Journal
Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach
Previous Article in Journal
Present Scenario of Long Non-Coding RNAs in Plants
Article Menu

Export Article

Open AccessArticle
Non-Coding RNA 2017, 3(2), 19; doi:10.3390/ncrna3020019

Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, Abelmoschus esculentus

Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021,Tamil Nadu, India
*
Author to whom correspondence should be addressed.
Received: 21 December 2016 / Revised: 10 March 2017 / Accepted: 24 March 2017 / Published: 31 March 2017
View Full-Text   |   Download PDF [1650 KB, uploaded 4 April 2017]   |  

Abstract

MicroRNAs (miRNAs) are crucial regulatory RNAs, originated from hairpin precursors. For the past decade, researchers have been focusing extensively on miRNA profiles in various plants. However, there have been few studies on the global profiling of precursor miRNAs (pre-miRNAs), even in model plants. Here, for the first time in a non-model plant—Abelmoschus esculentus with negligible genome information—we are reporting the global profiling to characterize the miRNAs and their associated pre-miRNAs by applying a next generation sequencing approach. Preliminarily, we performed small RNA (sRNA) sequencing with five biological replicates of leaf samples to attain 207,285,863 reads; data analysis using miRPlant revealed 128 known and 845 novel miRNA candidates. With the objective of seizing their associated hairpin precursors, we accomplished pre-miRNA sequencing to attain 83,269,844 reads. The paired end reads are merged and adaptor trimmed, and the resulting 40–241 nt (nucleotide) sequences were picked out for analysis by using perl scripts from the miRGrep tool and an in-house built shell script for Minimum Fold Energy Index (MFEI) calculation. Applying the stringent criteria of the Dicer cleavage pattern and the perfect stem loop structure, precursors for 57 known miRNAs of 15 families and 18 novel miRNAs were revealed. Quantitative Real Time (qRT) PCR was performed to determine the expression of selected miRNAs. View Full-Text
Keywords: miRNAs; pre-miRNAs sequencing; Abelmoschus esculentus; next generation sequencing; non-model plant miRNAs; pre-miRNAs sequencing; Abelmoschus esculentus; next generation sequencing; non-model plant
Figures

Figure 1a

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Velayudha Vimala Kumar, K.; Srikakulam, N.; Padbhanabhan, P.; Pandi, G. Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, Abelmoschus esculentus. Non-Coding RNA 2017, 3, 19.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Non-Coding RNA EISSN 2311-553X Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top